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NAMD

Description

NAMD is molecular dynamics simulation software using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms), develpoed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana–Champaign.

Versions

Following versions of NAMD are currently available:

  • Runtime dependencies:

You can load selected version (also with runtime dependencies) as a one module by following commands:

   module load NAMD/2.14-foss-2021a-CUDA-11.3.1


User guide

You can find the software documentation and user guide on the official NAMD website and/or NAMD's user guide.

Benchmarks

In order to better understand how NAMD utilises the available hardware on Devana and how to get good performance we can examine the effect on benchmark performance of the choice of the number of MPI ranks per node and OpenMP thread.

Following command has been used to run the benchmarks:

    mpiexec -np $ntmpi charmrun +p $ntomp +isomalloc_sync +setcpuaffinity namd2 +devices $gpu $trajectory 
where ntmpi and ntomp represent number of MPI ranks and OMP threads, respectively, and gpu represents IDs of used graphics processing units (0,1,2,3).

More information about these benchmarks systems, as well as downloadable input files, can be found here.

Info

"Single-node benchmarks have been run on local /work/ storage native to each compute node, which are generally faster than shared storage hosting /home/ and /scratch/ directories."

Benchmarks have been made on following systems:

Following file was used as input file for this benchmark:

NAMD Input file
#############################################################
## ADJUSTABLE PARAMETERS                                   ##
#############################################################
structure          stmv.psf
coordinates        stmv.pdb

#############################################################
## SIMULATION PARAMETERS                                   ##
#############################################################

# Input
paraTypeCharmm      on
parameters          par_all27_prot_na.inp
temperature         298

# Force-Field Parameters
exclude             scaled1-4
1-4scaling          1.0
cutoff              12.
switching           on
switchdist          10.
pairlistdist        13.5

# Integrator Parameters
timestep            1.0
nonbondedFreq       1
fullElectFrequency  4
stepspercycle       20

# Constant Temperature Control
langevin            on    ;# do langevin dynamics
langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
langevinTemp        298
langevinHydrogen    off    ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
useGroupPressure      yes ;# needed for rigidBonds
useFlexibleCell       no
useConstantArea       no

langevinPiston        on
langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
langevinPistonPeriod  100.
langevinPistonDecay   50.
langevinPistonTemp    298

cellBasisVector1     216.832    0.   0.
cellBasisVector2     0.   216.832    0.
cellBasisVector3     0.    0   216.832
cellOrigin           0.    0.   0.

PME                  on
PMEGridSizeX         216
PMEGridSizeY         216
PMEGridSizeZ         216

# Output
outputName          /home/<username>/stmv-output

outputEnergies      20
outputTiming        20

numsteps            50000

NAMD_single_node_perf

Numerical values for the benchmark are as follows:

GPU/MPI 1 2 4 8 16
1 1136 4652 13031 45043
2 712 3635 8673 26355 99093
4 477 3241 6471 16703 56104

Info

Remaining combinations of MPI/OMP were not feasible due to memory limit on the GPUs.


Thus, users are adviced to run NAMD with single MPI rank and vary only number of cpus assigned to this rank. It is important to understand that if user requests one mpi rank (#SBATCH --ntasks-per-node=1) and let us say 32 cpus (#SBATCH --cpus-per-task=32) he/she will be charged 32 BUs. This should be taken into account when requesting number of gpus (#SBATCH --gres=gpu:2), as half the cpus on accelerated node allows usage of two accelerated processing units.

Generally speaking, the best combination of requested resources, with respect to BUs, are as follows:

#SBATCH --ntasks-per-node= #SBATCH --cpus-per-task= #SBATCH --gres=gpu:
1 16 1
2 32 2
3 48 3
4 64 4

Example run script

You can copy and modify this script to namd_run.sh and submit job to a compute node by command sbatch namd_run.sh.

GPU partition

NAMD is compiled only in GPU-aware version and must be run on gpu partition.

GPU IDs

Variable DEVICES in the following script refers to IDs of gpus, which range from 0 to 3. Users are highly adviced to use this keyword and to NOT pass the variable to the argument but rather use plain text. If one wishes to perform calculation on 1 GPU this part of command should look like +devices 0, for 2 GPUS use +devices 0,1, etc.

    #!/bin/bash
    #SBATCH -J "namd_job"   # name of job in SLURM
    #SBATCH --account=<project> # project number
    #SBATCH --partition=gpu     # 
    #SBATCH --nodes=1       # gpu allocations allows only single node
    #SBATCH --ntasks-per-node=  # number of mpi ranks per node
    #SBATCH --cpus-per-task=    # number of cpus per mpi rank
    #SBATCH --time=hh:mm:ss     # time limit for a job
    #SBATCH -o stdout.%J.out    # standard output
    #SBATCH -e stderr.%J.out    # error output


    module load NAMD/2.14-foss-2021a-CUDA-11.3.1

    # Modify according to specific needs
    init_dir=`pwd`
    work_dir=/work/$SLURM_JOB_ID

    # Copy files over
    input_files=""
    output_files=""

    # Move to working directory
    cd $work_dir
    cp $input_files $work_dir/.

    # Start NAMD
    mpiexec -np ${SLURM_NTASKS} charmrun +p ${SLURM_CPUS_PER_TAKS} +isomalloc_sync +setcpuaffinity namd2 +devices ${DEVICES} <input_file>

    # Move files back
    cp $output_files $init_dir/.
Created by: Filip Holka, marek.steklac